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Calcium in PDB 6ymr: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

Enzymatic activity of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

All present enzymatic activity of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin, PDB code: 6ymr was solved by M.Kljajic, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.67 / 1.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.768, 92.768, 129.602, 90, 90, 120
R / Rfree (%) 13.5 / 17.8

Other elements in 6ymr:

The structure of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin (pdb code 6ymr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin, PDB code: 6ymr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ymr

Go back to Calcium Binding Sites List in 6ymr
Calcium binding site 1 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:14.3
occ:1.00
 O E:GLN61 2.3 13.3 1.0
O E:HOH582 2.3 17.0 1.0
O E:HOH709 2.4 16.4 1.0
OD1 E:ASP57 2.4 14.5 1.0
OD1 E:ASP59 2.4 14.7 1.0
O E:HOH572 2.4 15.4 1.0
OD2 E:ASP57 2.6 14.0 1.0
CG E:ASP57 2.8 13.7 1.0
H E:GLN61 3.3 14.8 1.0
CG E:ASP59 3.4 15.5 1.0
C E:GLN61 3.5 13.1 1.0
H E:ASP59 3.5 16.4 1.0
HB2 E:GLN61 3.7 19.9 1.0
OD2 E:ASP59 3.8 18.2 1.0
O E:HOH623 4.0 18.7 1.0
N E:GLN61 4.0 12.4 1.0
HA E:PHE62 4.0 15.2 1.0
CA E:GLN61 4.2 13.5 1.0
H E:ALA58 4.3 16.1 1.0
CB E:ASP57 4.3 13.6 1.0
N E:ASP59 4.3 13.7 1.0
H E:ASN60 4.4 15.4 1.0
CB E:GLN61 4.4 16.6 1.0
O E:HOH671 4.4 15.1 1.0
N E:PHE62 4.5 13.4 1.0
CB E:ASP59 4.6 13.6 1.0
OD2 E:ASP67 4.6 13.4 1.0
O E:HOH543 4.6 13.8 1.0
O E:HOH752 4.7 35.0 1.0
N E:ASN60 4.7 12.8 1.0
HB2 E:ASP57 4.7 16.3 1.0
N E:ALA58 4.7 13.5 1.0
CA E:PHE62 4.7 12.7 1.0
HB3 E:ASP57 4.8 16.3 1.0
H E:PHE63 4.8 16.6 1.0
CA E:ASP59 4.8 12.5 1.0
HA E:ASP57 4.8 16.1 1.0
HB3 E:ALA58 4.9 19.3 1.0
HB3 E:GLN61 4.9 19.9 1.0
C E:ASP59 4.9 13.5 1.0

Calcium binding site 2 out of 4 in 6ymr

Go back to Calcium Binding Sites List in 6ymr
Calcium binding site 2 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:14.9
occ:1.00
 O E:GLU187 2.4 15.2 1.0
OD2 E:ASP138 2.4 13.3 1.0
O E:HOH540 2.4 14.8 1.0
OD1 E:ASP185 2.4 15.6 1.0
OE1 E:GLU177 2.5 14.3 1.0
OE2 E:GLU190 2.5 15.9 1.0
OE1 E:GLU190 2.5 14.4 1.0
OE2 E:GLU177 2.8 14.9 1.0
CD E:GLU190 2.8 16.1 1.0
CD E:GLU177 2.9 13.9 1.0
CG E:ASP138 3.4 14.3 1.0
C E:GLU187 3.4 15.4 1.0
CG E:ASP185 3.5 16.8 1.0
HB3 E:ASP138 3.6 16.1 1.0
HA E:ILE188 3.6 18.2 1.0
H E:GLU187 3.7 20.9 1.0
CA E:CA404 3.8 16.3 1.0
H E:GLY189 3.8 17.4 1.0
OD2 E:ASP185 3.8 18.4 1.0
HB2 E:GLU187 3.9 24.8 1.0
CB E:ASP138 4.0 13.4 1.0
O E:ASP185 4.1 16.5 1.0
H E:GLU190 4.2 17.4 1.0
H E:ASP185 4.2 20.9 1.0
N E:GLU187 4.2 17.4 1.0
N E:ILE188 4.2 14.6 1.0
HB2 E:ASP138 4.3 16.1 1.0
OD1 E:ASP138 4.3 15.0 1.0
CA E:GLU187 4.3 17.6 1.0
CA E:ILE188 4.3 15.2 1.0
CG E:GLU190 4.3 16.4 1.0
HD13 E:ILE188 4.3 20.9 1.0
CG E:GLU177 4.4 14.9 1.0
N E:GLY189 4.5 14.5 1.0
O E:HOH539 4.5 19.4 1.0
C E:ASP185 4.6 16.6 1.0
CB E:GLU187 4.6 20.7 1.0
HG3 E:GLU190 4.6 19.6 1.0
HB2 E:GLU177 4.7 18.5 1.0
HB3 E:GLU177 4.7 18.5 1.0
CB E:ASP185 4.7 17.1 1.0
N E:ASP185 4.8 17.5 1.0
HG2 E:GLU190 4.8 19.6 1.0
C E:ILE188 4.8 14.7 1.0
HG2 E:GLU177 4.8 17.9 1.0
HA E:THR174 4.9 17.3 1.0
O E:HOH524 4.9 18.5 1.0
CB E:GLU177 4.9 15.5 1.0
HG3 E:GLU177 4.9 17.9 1.0
HB3 E:GLU190 5.0 19.8 1.0
CA E:ASP185 5.0 16.8 1.0
N E:GLU190 5.0 14.5 1.0

Calcium binding site 3 out of 4 in 6ymr

Go back to Calcium Binding Sites List in 6ymr
Calcium binding site 3 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:16.3
occ:1.00
 O E:ASN183 2.3 18.6 1.0
OE2 E:GLU190 2.3 15.9 1.0
O E:HOH524 2.4 18.5 1.0
OD2 E:ASP185 2.4 18.4 1.0
OE2 E:GLU177 2.4 14.9 1.0
O E:HOH546 2.4 19.7 1.0
CG E:ASP185 3.2 16.8 1.0
CD E:GLU177 3.2 13.9 1.0
CD E:GLU190 3.3 16.1 1.0
C E:ASN183 3.5 19.7 1.0
HG3 E:GLU190 3.6 19.6 1.0
HA E:PRO184 3.6 23.2 1.0
OD1 E:ASP185 3.6 15.6 1.0
HB2 E:ASN183 3.7 30.3 1.0
OE1 E:GLU177 3.8 14.3 1.0
HG2 E:GLU190 3.8 19.6 1.0
CA E:CA403 3.8 14.9 1.0
CG E:GLU190 3.8 16.4 1.0
HB3 E:ASN183 3.8 30.3 1.0
H E:ASP185 4.1 20.9 1.0
OD2 E:ASP191 4.1 20.2 1.0
CA E:PRO184 4.1 19.4 1.0
CB E:ASN183 4.2 25.3 1.0
N E:ASP185 4.2 17.5 1.0
HG2 E:GLU177 4.2 17.9 1.0
CG E:GLU177 4.2 14.9 1.0
C E:PRO184 4.3 19.7 1.0
N E:PRO184 4.3 19.8 1.0
OD1 E:ASP191 4.3 19.7 1.0
OE1 E:GLU190 4.3 14.4 1.0
HG3 E:GLU177 4.3 17.9 1.0
HB3 E:ASP185 4.3 20.5 1.0
CB E:ASP185 4.4 17.1 1.0
O E:LYS182 4.4 23.8 1.0
O E:HOH745 4.4 48.9 1.0
CA E:ASN183 4.5 23.3 1.0
O E:HOH721 4.5 50.4 1.0
CG E:ASP191 4.6 19.2 1.0
O E:PRO184 4.9 20.7 1.0
CA E:ASP185 4.9 16.8 1.0

Calcium binding site 4 out of 4 in 6ymr

Go back to Calcium Binding Sites List in 6ymr
Calcium binding site 4 out of 4 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:19.2
occ:1.00
 O E:ILE197 2.3 26.7 1.0
OG1 E:THR194 2.3 19.7 1.0
O E:TYR193 2.3 19.1 1.0
O E:HOH683 2.4 28.3 1.0
OD1 E:ASP200 2.4 22.0 1.0
O E:HOH576 2.4 18.8 1.0
O E:THR194 2.4 20.5 1.0
C E:THR194 3.2 19.4 1.0
C E:TYR193 3.3 18.4 1.0
CB E:THR194 3.4 19.6 1.0
HB E:ILE197 3.4 34.6 1.0
CG E:ASP200 3.5 22.3 1.0
C E:ILE197 3.5 28.0 1.0
H E:ILE197 3.6 35.4 1.0
CA E:THR194 3.6 18.7 1.0
HB E:THR194 3.6 23.5 1.0
OD2 E:ASP200 3.8 22.7 1.0
N E:THR194 3.8 18.4 1.0
H E:ASP200 3.9 27.4 1.0
HA E:SER198 4.1 38.5 1.0
HB3 E:TYR193 4.1 21.6 1.0
CA E:ILE197 4.2 28.1 1.0
HD2 E:TYR193 4.2 25.6 1.0
CB E:ILE197 4.2 28.9 1.0
N E:ILE197 4.2 29.5 1.0
N E:PRO195 4.3 20.9 1.0
HA E:PRO195 4.4 28.2 1.0
O E:HOH713 4.4 50.6 1.0
HG22 E:ILE197 4.4 33.8 1.0
O E:ASP200 4.5 19.7 1.0
O E:HOH717 4.5 37.0 1.0
N E:SER198 4.5 30.9 1.0
CA E:TYR193 4.5 16.8 1.0
HA E:THR194 4.6 22.4 1.0
CG2 E:THR194 4.6 21.1 1.0
N E:ASP200 4.7 22.9 1.0
CA E:SER198 4.7 32.2 1.0
O E:GLU190 4.7 16.4 1.0
H E:THR194 4.7 22.1 1.0
CB E:TYR193 4.7 18.1 1.0
CD2 E:TYR193 4.7 21.3 1.0
CA E:PRO195 4.7 23.6 1.0
CB E:ASP200 4.8 21.9 1.0
C E:ASP200 4.8 18.8 1.0
HG23 E:THR194 4.8 25.2 1.0
H E:GLY199 4.8 33.1 1.0
HG21 E:THR194 4.9 25.2 1.0
CG2 E:ILE197 4.9 28.2 1.0
C E:SER198 4.9 30.9 1.0
CA E:ASP200 5.0 20.8 1.0

Reference:

M.Kljajic, H.-D.Gerber, A.Heine, G.Klebe. Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin To Be Published.
Page generated: Wed Jul 9 20:23:43 2025

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